You could use the plain old substr and length functions instead of Regular Expressions.

use strict;

while (<DATA>)
{
    chomp;
    my ($c1, $c2) = (substr($_,0,1), substr($_,length($_)-1,1));

    if ($c1 == '(' && $c2 != ')') {
        substr($_,0,1) = undef;
    } elsif ($c1 != '(' && $c2 == ')') {
        substr($_,length($_)-1,1) = undef;
    }
    
    print "$_\n";
}

__DATA__
(1.3.56.84
56.38.m.26)
(56.2.3.59)
[download]

And the output is

1.3.56.84
56.38.m.26
(56.2.3.59)
[download]